Bio::Tools::Run::Primer3 Create input for and work with the output from the program primer3
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Perl module perl output program primer3 primer3 output primer3

Bio::Tools::Run::Primer3 Description

Create input for and work with the output from the program primer3 Bio::Tools::Run::Primer3 is a Perl module to create input for and work with the output from the program primer3.SYNOPSISBio::Tools::Primer3 creates the input files needed to design primers using primer3 and provides mechanisms to access data in the primer3 output files.This module provides a bioperl interface to the program primer3. See http://frodo.wi.mit.edu/primer3/primer3_code.html for details and to download the software. This module should work for primer3 release 1 but is not guaranteed to work with earlier versions. # design some primers. # the output will be put into temp.out use Bio::Tools::Run::Primer3; use Bio::SeqIO; my $seqio = Bio::SeqIO->new(-file=>'data/dna1.fa'); my $seq = $seqio->next_seq; my $primer3 = Bio::Tools::Run::Primer3->new(-seq => $seq, -outfile => "temp.out", -path => "/usr/bin/primer3_core"); # or after the fact you can change the program_name $primer3->program_name('my_suprefast_primer3'); unless ($primer3->executable) { print STDERR "primer3 can not be found. Is it installed? "; exit(-1) } # what are the arguments, and what do they mean? my $args = $primer3->arguments; print "ARGUMENT MEANING "; foreach my $key (keys %{$args}) {print "$key ", $$args{$key}, " "} # set the maximum and minimum Tm of the primer $primer3->add_targets('PRIMER_MIN_TM'=>56, 'PRIMER_MAX_TM'=>90); # design the primers. This runs primer3 and returns a # Bio::Tools::Run::Primer3 object with the results $results = $primer3->run; # see the Bio::Tools::Run::Primer3 pod for # things that you can get from this. For example: print "There were ", $results->number_of_results, " primers ";Bio::Tools::Run::Primer3 creates the input files needed to design primers using primer3 and provides mechanisms to access data in the primer3 output files.This module provides a bioperl interface to the program primer3. See http://www-genome.wi.mit.edu/genome_software/other/primer3.html for details and to download the software.Developer commentsThis module is based on one written by Chad Matsalla. I have ripped some of his code, and added a lot of my own. Requirements: · Perl

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